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Setup

What is Lamington?

This application provides a user-friendly GUI wrapper for Core Hunter, enabling you to:

  • Create core diversity sets from genetic population data
  • Filter genotypes and samples
  • Visualize data through PCA plots
  • Detect genetic outliers
  • Generate optimized core subsets

The tool streamlines the process of genetic diversity analysis through an intuitive interface.

image

Prerequisites

  • Any machine with Docker installed. See Docker for more information.

  • Your own terminal application

Setup

In your terminal, run the following command:

docker run -it -p 127.0.0.1:3838:3838 plantinformaticscollaboration/lamington

Note

When this command is run for the first time, it will take a few minutes to download the docker image from dockerhub.

When the application is successfully started, you will see the following output in the terminal:

Output
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> shiny::runApp('/root/app',host = '0.0.0.0', port=3838)
Loading required package: shiny
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable


Listening on http://0.0.0.0:3838
Loading required namespace: plotly
Failed with error:  ‘there is no package called ‘plotly’’

Accessing the Lamington server

Open your web browser and navigate to http://localhost:3838.

Stopping the Lamington server

To stop the Lamington server, press Ctrl+C in the terminal.

Additional run options

The following options can be used to run the application:

Subsituting -it with -d will run the application in detached mode. Meaning that the application will run in the background and you will not be able to be stopped by pressing Ctrl+C.

Additionally if you want to run the application with mounted volumes, you can use the following command:

docker run -it -p 127.0.0.1:3838:3838 -v '/path/to/your/data/VCFs:/root/VCFs' -v '/path/to/your/data/GDS:/root/GDS' plantinformaticscollaboration/lamington

This will mount the /path/to/your/data/VCFs directory to the /root/VCFs directory in the container and the /path/to/your/data/GDS directory to the /root/GDS directory in the container.